>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

Probab=90.03 E-value=0.86 Score=25.37 Aligned_cols=57 Identities=19% Similarity=0.300 Sum_probs=39.4 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCC Q ss_conf 877627751468874658854887788379999500023588----446899889999998699971 Q gi|254780913|r 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGK 64 (78) Q Consensus 2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk 64 (78) T Consensus 3 iv~G~V~~i~~---fG~FV~l---~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD~~~r 63 (68) T cd04472 3 IYEGKVVKIKD---FGAFVEI---LPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGR 63 (68) T ss_pred EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCC T ss_conf 99999999973---2999995---7996248886893456546988907899999999999999997

HHsearch alignment for GI: 254780913 and conserved domain: cd04472